Status of Fish Populations and Habitat in Thunder Bay The status of fish populations and their habitat in the Thunder Bay Area of Concern March 26, 2015 Prepared for: Environment Canada Prepared by: Terry Marshall Marshall Consulting i Status of Fish Populations and Habitat in Thunder Bay Table of Contents List of Tables ................................................................................................................................................ iii List of Figures ............................................................................................................................................... iii 1 Introduction ......................................................................................................................................... 1 2 Description of Issues ............................................................................................................................ 2 3 4 5 6 2.1 Loss of fish habitat ........................................................................................................................ 2 2.2 Degradation of fish populations ................................................................................................... 3 Remedial Actions .................................................................................................................................. 4 3.1 Stage 2 RAP Projects ..................................................................................................................... 4 3.2 Science and Monitoring Projects ................................................................................................ 10 Status of Fish Habitat ......................................................................................................................... 10 4.1 Delisting Criteria: A Review ......................................................................................................... 11 4.2 Outstanding habitat issues ......................................................................................................... 15 Status of Fish Populations .................................................................................................................. 15 5.1 Delisting Criteria.......................................................................................................................... 16 5.2 Fish Community .......................................................................................................................... 16 5.3 Lake Trout ................................................................................................................................... 18 5.4 Lake Whitefish............................................................................................................................. 20 5.5 Lake Sturgeon, Walleye and Brook Trout ................................................................................... 22 5.5.1 Lake Sturgeon...................................................................................................................... 22 5.5.2 Walleye ............................................................................................................................... 24 5.5.3 Brook Trout ......................................................................................................................... 25 Conclusions ........................................................................................................................................ 26 6.1 Fish Habitat ................................................................................................................................. 26 6.2 Fish Populations .......................................................................................................................... 27 7 Literature Cited .................................................................................................................................. 29 8 Appendix l: Fishes of Thunder Bay Harbour Area ............................................................................. 33 ii Status of Fish Populations and Habitat in Thunder Bay List of Tables Table 1: Remedial activities identified in Stage 2 RAP report (Vander Wal et al. 2004) as they relate to recommendations from the Stage 1 RAP (Thunder Bay RAP Team 1991). The proponents of these projects are as follows: Canadian Pacific Railway (CPR); Department of Fisheries and Oceans (DFO); Environment Canada (EC); Environment Canada’s Great Lakes Cleanup Fund (GLCUF); Great Lakes Sustainability Fund (GLSF); Health Canada (HC); Industry Canada (IC); Lake Superior Programs Office (LSPO); Ontario Ministry of Natural Resources and Forestry (MNRF); Ontario Ministry of the Environment and Climate Change (MOECC); Public Advisory Committee (PAC); Transport Canada (TC) ... 5 Table 2: Recent Science and Monitoring projects, ongoing or completed................................................. 10 Table 3: Comparison of nearshore fish species occurrence both within and immediately outside of the AOC based on FCIN catches. Species non-native to Lake Superior are indicated with an asterisk. .......... 17 Table 4: Statistics related to delisting criteria for lake trout from annual FCIN sampling (2009-2014) within the AOC. Values for Length at Age 7 include samples from area adjacent to AOC to provide adequate sample sizes. ............................................................................................................................... 19 Table 5: Summary table illustrating status of fish habitat delisting criteria within Thunder Bay AOC. A green check mark indicates that work has been completed to address the problem with effective results. A yellow check mark indicates that the project has been completed, but the results are not satisfactory. A red check mark indicates a lack of progress on this issue. ...................................................................... 27 Table 6: Overview of fish population status within the Thunder Bay AOC. A green check mark indicates that the delisting criteria are completely satisfied; a yellow check mark indicates that habitat issues for the species persist but are soon to be rectified; a red check mark indicates that the population remains depressed for a variety of reasons.............................................................................................................. 28 List of Figures Figure 1: The Thunder Bay Area of Concern and associated features (Environment Canada). ................... 2 Figure 2: Location of completed fish habitat remedial projects in the vicinity of the lower Kaministiquia River (upper) and Thunder Bay harbour (lower). ......................................................................................... 9 Figure 3: Relative abundance (catch per unit effort) of nearshore fish species sampled inside (blue bars) and outside (red bars) of the AOC. Data represents means from FCIN averaged over a six year period (2009-2014), omitting rare species. ............................................................................................................ 18 Figure 4: Lake trout mean total length at age from FCIN samples 2009-2014. .......................................... 19 Figure 5: Age frequency histogram for lake trout sampled inside (red bars) and outside (blue bars) of the AOC in FCIN (2009-2013). ........................................................................................................................... 20 Figure 6: Total annual mortality of lake whitefish as indicated from commercial catch and fish community index nets. Mortality was calculated through linear regression of the descending limb of the catch curve from modal age onward where sample sizes exceeded four fish per age class (Ricker 1975). .................................................................................................................................................................... 21 Figure 7: Lake whitefish age structure from commercial catch all years. .................................................. 22 iii Status of Fish Populations and Habitat in Thunder Bay 1 Introduction The Thunder Bay AOC is one of 43 Great Lakes Areas of Concern identified within the 1987 amendment to the Great Lakes Water Quality Agreement, requiring a Remedial Action Plan (RAP) to be developed. The Thunder Bay Area of Concern (AOC) extends approximately 28 km along the shoreline of Lake Superior and up to nine kilometres offshore from the City of Thunder Bay (Figure 1). It is exposed to the open waters of Lake Superior along its southern and eastern boundaries, while the Bay extends beyond the AOC to the north. Thunder Bay was classified an AOC because of a variety of problems associated with heavy metals, toxic organics, contaminated sediments, fish consumption advisories, impacted biota, beach closings, and conventional pollutants. It has experienced ecosystem impairments as a result of waterfront development, industrial and municipal wastewater discharge, and the hydroelectric development of urban tributaries. The Stage 1 (Definition of Problem) and Stage 2 (Remedial Strategies) components of the Thunder Bay RAP have been completed. We are now moving into the next stage which requires documenting evidence that beneficial uses of the area have been restored. This report documents the current status of fish populations and their habitat, which were deemed to be impaired within the Stage 2 RAP report. The issues responsible for their impairment are reviewed and the remedial actions taken to address these impairments are summarized. The various habitat-related projects undertaken through the RAP process are evaluated for their completeness and effectiveness, and outstanding issues are identified. Additionally, fish populations are evaluated against delisting criteria, developed earlier through the RAP process, to determine whether impairments still exist. If so, actions required to address these impairments are suggested. 1 Status of Fish Populations and Habitat in Thunder Bay Figure 1: The Thunder Bay Area of Concern and associated features (Environment Canada). 2 Description of Issues 2.1 Loss of fish habitat Fish habitat in the Thunder Bay AOC was severely degraded through the 1900’s by shoreline development along the waterfront and lower Kaministiquia River system, which includes the McKellar and Mission Rivers. Much of the natural wetlands disappeared, and with them the loss of spawning, nursery, and forage habitat for a number of fish species that they supported. A break-wall was constructed that affected the natural cleansing of shoreline areas through wave and current action. Water management practices related to hydropower, flood control, and aesthetics also affected the productivity of the aquatic community downstream. The lower Kaministiquia River has suffered considerable environmental degradation through the years. Prior to 1920, the river supported a fall run of lake whitefish numbering in the tens of thousands. The collapse of this spawning population was attributed to dredging operations and the daily dumping of 500,000 bushels of grain screenings into the river near the site of the current Resolute Forest Products mill (Goodier 1981). Organic waste continued to be deposited at this site from pulp mill operations. This 2 Status of Fish Populations and Habitat in Thunder Bay contributed to a high biochemical oxygen demand (BOD) of sediments which created a zone of low dissolved oxygen within the river. During periods of low flows this effectively prevented the passage of fish (Thunder Bay RAP Team 1991). This problem was significantly reduced when secondary treatment of the kraft and newsprint mill at the (now) Resolute Forest Product mill was initiated in 1993. A number of other point sources of pollutants have contributed to the degradation of aquatic habitat. The City of Thunder Bay’s wastewater plant released 109 million liters per day of effluent into the mouth of the Kaministiquia River with only primary treatment until 2005. Secondary treatment was put in place at that time along with ultraviolet disinfection of wastewater. The direct discharge of untreated wastewater along with leachate and surface run-off from industrial wood product sites has resulted in large areas of contaminated sediments within the harbour. These represent sources of significant toxic pollutants, including dioxins, furans, pentachlorophenol, creosote, heavy metals and PAHs. Sediment remediation has occurred at the Northern Wood Preservers site (NOWPARC project) which was the most significant area of contamination. The former Cascades Fine Paper property (Thunder Bay North Harbour) has 22 ha of sediments comprised of waste wood products that are substantially elevated in mercury and other contaminants (Grapentine 2011). In addition, areas east of the Mission and McKellar deltic islands and the SmurfitStone Container Canada Inc. site (formerly Thunder Bay Packaging, located north of the break wall outside of the Thunder Bay Harbour) also have sediment contamination issues. Dredging operations are a commonplace activity in the AOC. Historically, they have had a significant impact on aquatic habitat both at dredging sites and at the disposal locations of dredged materials. Aquatic habitat in the navigational channels has been considerably altered through this activity. Traditional lake trout and lake herring spawning areas near the Welcome Islands may have been damaged by the disposal of dredged materials (Sutton 1975). Dredging operations continue in the harbour today, but with regulatory tools such as the Provincial Sediment Quality Guidelines adopted in 1993, this activity is expected to be more benign to the aquatic ecosystem (Nicholson 2013). 2.2 Degradation of fish populations Thunder Bay supports a diverse fish community with 55 confirmed species (Foster 2012; Appendix 1). However, this community has changed dramatically from its historic norm. For over a century, aquatic and terrestrial habitat was modified or destroyed in the Thunder Bay AOC and surrounding watershed with the advent of industrial, residential, and recreational development. Dredging, channelization, and the release of a number of pollutants, as discussed above, eliminated a significant portion of the quality habitat along the waterfront. Habitat degradation resulted in a loss of species abundance and diversity, reduced recreational opportunities, and a decline in the aesthetic value of the harbour and its tributaries. 3 Status of Fish Populations and Habitat in Thunder Bay Fish populations also declined as a result of commercial and recreational over-exploitation, the introduction of exotic species, and the accumulation of toxic chemicals. Point sources of pollution impacted aquatic habitat and fish populations in the Thunder Bay harbour and lower Kaministiquia River. Discharge periodically exceeded the assimilative capacity of the river, resulting in restrictions to fish movement and intermittent fish kills as recent as the late 1980’s (Thunder Bay RAP Team 1991). Many of these historical impacts have now been mitigated through recent habitat restoration initiatives under taken by the RAP. Exotic species have also affected fish populations, with 15 non-native fish species now documented within the Thunder Bay AOC (Foster 2012; Appendix 1). The early introduction of pacific salmon and the invasion of rainbow smelt and sea lamprey altered the dynamics of the native coldwater fish community (Lawrie and Rahrer 1972). More recently, introductions of ruffe, zebra mussels (Dreissena polymorpha), rusty crayfish (Orconectes rusticus), 3 and 4 spine sticklebacks, Eurasian milfoil, and spiny water fleas (Bythotrephes cederstroemi) have become a growing concern for northern areas of Lake Superior. There is a high potential for additional invasive species to appear in the AOC, as several major shipping routes terminate in the harbour, increasing the likelihood of introduction via ballast water exchange (Grigorovich et al. 2003; Schloesser et al. 2012). In addition, the Kaministiquia River flowing into the harbour area provides relatively rich and warm waters that are conducive to the survival of potential invasive species. The use of chemical lampricides in Thunder Bay tributaries may also have had a detrimental effect on the aquatic communities of the AOC (Boogaard et al. 2003). Lampricides were first applied in the Great Lakes in 1958. The Kaministiquia, Neebing and McIntryre rivers continue to receive periodic treatment with the chemical TFM. 3 Remedial Actions 3.1 Stage 2 RAP Projects The Stage 2 RAP identified Beneficial Use Impairments (BUIs) related to fish and wildlife and proposed a strategy to remediate these (Vander Wal et al. 2004). The strategy consisted of four recommendations: Recommendation 1-1: Increase the extent of productive aquatic and terrestrial habitat by rehabilitating and protecting wetland and riparian environments, and by enforcing existing environmental legislation. Recommendation 1-2: Prevent the loss of aquatic migration corridors. 4 Status of Fish Populations and Habitat in Thunder Bay Recommendation 1-3: Rehabilitate ecosystem function and structure in order to support a diverse, healthy, self-sustaining biological community. This will ultimately require the virtual elimination of persistent, bioaccumulative and toxic substances (bearing in mind social and economic factors) to ensure that the water quality and sediment conditions in both the lower Kaministiquia River and in Thunder Bay Harbour provide a healthy and hospitable environment. Recommendation 1-4: Prevent impacts on fish and wildlife population dynamics including those produced by the introduction of exotics. A number of specific remedial actions were identified which would contribute to each of these recommendations. Most of these actions were completed, although a few are pending. Some have not achieved their objectives (as highlighted in Table 1). The proponents, the status and the cost of each project are summarized in Table 1. The location of the key habitat projects are identified in Figure 2. Table 1: Remedial activities identified in Stage 2 RAP report (Vander Wal et al. 2004) as they relate to recommendations from the Stage 1 RAP (Thunder Bay RAP Team 1991). The proponents of these projects are as follows: Canadian Pacific Railway (CPR); Department of Fisheries and Oceans (DFO); Environment Canada (EC); Environment Canada’s Great Lakes Cleanup Fund (GLCUF); Great Lakes Sustainability Fund (GLSF); Health Canada (HC); Industry Canada (IC); Lake Superior Programs Office (LSPO); Ontario Ministry of Natural Resources and Forestry (MNRF); Ontario Ministry of the Environment and Climate Change (MOECC); Public Advisory Committee (PAC); Transport Canada (TC) Project Code Project Title Status Proponent Cost Recommendation 1-1: Increase the extent of productive aquatic and terrestrial habitat by rehabilitating and protecting wetland and riparian environments, and by enforcing existing environmental legislation. FWH-1 Rehabilitation of Degraded Walleye Spawning Habitat at the Current River Estuary Construction completed December 1991; assessment of adult walleye abundance ongoing. EC/GLCUF, MNRF, MOECC, and DFO $37,500 for construction, and $42,000 for assessment. FWH-2 Alteration of Shoreline to Restore Habitat Diversity at the Neebing-McIntyre Floodway Completed in 1991, with additional trail work completed in 2001. EC/GLCUF, MNRF, MOECC, and DFO $109,889 for construction, and $74,830 for assessment FWH-3 Island Creation and Habitat Rehabilitation at the Mouth of McVicar Creek. Phase I: Bank Stabilization and Substrate Enhancement. Phase II: Island Creation. Phase I construction completed in 1992, with additional tree planting in 1993; Phase II completed in 1993. EC/GLCUF, MNRF, MOECC, and DFO Phase I: $215,000. Phase II: $380,000. Assessment; $17,200. 5 Status of Fish Populations and Habitat in Thunder Bay FWH-4 Redesign Waterfront Park to Protect and Enhance Shoreline of the Kaministiquia River, Including Scenic Overlook, Promenade, and Additional 500m of Park. Overlook completed in 1992; Promenade completed in 1994. Construction of further 500m of park has been completed. LSPO (in past), EC/GLCUF Overlook: $1.3 million. Promenade: $550,000. Estimated $1.5 million for project completion. FWH-5 Creation of Embayments in the McKellar River to Restore Productive Littoral Habitat Construction of embayments completed in 1994. Site monitored in first two seasons after construction EC/GLCUF, MNRF, MOECC, and DFO Construction: $607,800. DFO, LRCA, MNRF, North Shore Steelhead Association. Fish ladder $344,000. Pools: $62,500. Fish transfer: less than $500 per year. Bowater Bowater has spent approximately $68 million on environmental controls and upgrades since 1991. Recommendation 1-2: Prevent the loss of aquatic migration corridors. FWH-6 FWH-7 Improving Salmonid Access to the Upper Reaches of the Current River Fish ladder completed in 1992, pool construction in 1995, and fish transfer program from 1993 to 1995 and in 1997. The project, however, has not achieved its objectives. Alleviating Water Quality Barriers to Fish Migration in the Kaministiquia River Secondary treatment at kraft (1991) and newsprint (1995) mills complete. Bowater switched to 100% chlorine dioxide in 1994. Recommendation 1-3: Rehabilitate ecosystem function and structure in order to support a diverse, healthy, self-sustaining biological community. This will ultimately require the virtual elimination of persistent, bioaccumulative and toxic substances (bearing in mind social and economic factors) to ensure that the water quality and sediment conditions in both the lower Kaministiquia River and in Thunder Bay Harbour provide a healthy and hospitable environment. Northern Wood Preservers Alternative Remediation Concept (NOWPARC) Project Primary components completed from 1997 to 2002 AbitibiConsolidated Inc., Canadian National Railway Co., Northern Sawmills Inc., MOECC, and EC/GLSF. FWP-1 Directed Recovery of Native Fish Species Status of Lake Sturgeon in Lake Superior report completed (1996); Lake Sturgeon Rehabilitation Plan completed (2003); sturgeon population assessment in the Kaministiquia River has been ongoing since 1998 EC/GLSF, DFO, State and Tribal Governments, MNRF $100,000 (January 2004) PS-1 Secondary Treatment at the Bowater Pulp and Paper Mill Completed. See Action FWH-7 Bowater Approximately $68 million PS-2 Upgrades at Thunder Bay Terminals Upgrades completed. Monitoring of groundwater recommended. Thunder Bay Terminals Cost not available NPS-1 Approximately $20 million. 6 Status of Fish Populations and Habitat in Thunder Bay PS-3 Process Upgrades at Ontario Power Generation - Thunder Bay Generating Station Process upgrades completed. Monitoring environmental improvements due to OPG’s development of Mission Island Marsh is recommended (see Action PSM-3). Ontario Power Generation Thunder Bay Generating Station Cost not available PS-4 Secondary Treatment at Abitibi- Consolidated Ongoing cycles of the federal EEM program AbitibiConsolidated Cost not available PS-5 Redirect Stormwater Outlet and Remediate Residual Oil from CPR Water/Oil Separator The design to redirect the stormwater discharge through a series of vegetated cells was completed In 1998. The separator has been removed, and some remediation has occurred. However, residual hydrocarbon accumulations still remain on the property. CPR Cost not available PS-6 Secondary Treatment at Water Pollution Control Plant Completed 2005-2006 City of Thunder Bay, MOECC, ECGLSF, IC $73.6M for upgrade to secondary PS-8 Process Improvements at Smurfit-Stone Container Canada Inc. (formerly Thunder Bay Packaging) Implementation of secondary treatment completed in summer of 1997. Plant closed Dec. 3, 2003. Smurfit-Stone Container Canada Inc. Cost not available NPS-2 Develop a Management Plan for Mercury Contaminated Sediments at Cascades Fine Paper Group A 2003 mercury study has been completed, as has a 2011 feasibility study of sediment management options. Ecological and Human Health Ecological Assessments are currently underway. Cascades Fine Papers Group, EC, MOECC Cost not available NPS-G1 Develop and Implement Plans to Remediate Any Remaining Non-Point Sources of Contaminants Which are Contributing Significantly to the Fish and Wildlife Related Impairments Not yet implemented. A Stormwater Master Plan for the City of Thunder Bay is in its final stages of development. EC, MOE, NWRI, DFO, HC, City of Thunder Bay PS-G1 Develop and Implement Plans to Remediate Any Remaining Point Sources of Contaminants Which are Contributing Significantly to the Fish and Wildlife Related Impairments Not yet implemented. A recent sediment study by MOECC of areas with historic industrial discharge is soon to be released. EC, MOE, NWRI, DFO, HC Recommendation 1-4: Prevent impacts on fish and wildlife population dynamics including those produced by the introduction of exotics. 7 Status of Fish Populations and Habitat in Thunder Bay FWP-2 Initiative to Devise Alternate Means to Control Sea Lamprey Fishway and sea lamprey barrier completed 1993, but proved ineffective and was decommissioned in 2005 Sea Lamprey Control Centre, EC/GLCUF, DFO Operation of lamprey trap: $2,500/yr FWP-3 Preventing Further Introductions of Exotic Species Background report Ballast Water: State of the Science, Guidelines and Regulations completed 1994. DFO, TC, MNR, PAC, State and Tribal Governments. $10,000 Recommendation 1-1, 1-2, and 1-3: In combination PS-7 Thunder Bay Pollution Prevention and Control Plan Phase I and II complete with an implementation plan to address short and long term needs. Canada-Ontario Infrastructure Program, City of Thunder Bay. $73.6M for upgrade to secondary treatment, $19.7M to reduce surface water and infiltration water, $2.6M for sewer upgrades, $1.3M for facilities to treat filter backwash water at water treatment plant. FWH-8 Test Guidelines for Collecting Baseline Aquatic Habitat Data Aquatic habitat survey completed 1994. DFO, MNRF $20,000.00 Develop Watershed Management Plan for the Slate River Completed: Draft management plan completed 1998. Remaining: The Watershed Management Plan for the Slate River needs to be reviewed by the members of the PAC and by the Lakehead Region Conservation Authority prior to its implementation under Action FWH-10. Implementation will be conditional upon the participation of the municipal government. EC/GLCUF, DFO, Lakehead Region Conservation Authority (LRCA) $120,000 FWH-9 8 Status of Fish Populations and Habitat in Thunder Bay Figure 2: Location of completed fish habitat remedial projects in the vicinity of the lower Kaministiquia River (upper) and Thunder Bay harbour (lower). 9 Status of Fish Populations and Habitat in Thunder Bay 3.2 Science and Monitoring Projects Research and monitoring by government agencies and partner organizations is an important component of the RAP process for understanding and measuring the success of restoration efforts. As a follow-up to some of the restoration activities described above and to fulfill other monitoring requirements as part of the delisting criteria for fish populations, a number of initiatives have been undertaken or are ongoing (Table 2). Table 2: Recent Science and Monitoring projects, ongoing or completed. Project Code Project Title Status Proponent Cost SM-FWP-1 Fish Community Index Netting Program Ongoing Monitoring Initiative (Beginning in 2009) MNR/EC $16,000/year SM-FWP-2 Kaministiquia River Walleye Radio Telemetry Project Completed Monitoring Initiative (2009 - 2014) MNR/EC $120,000 SM-FWP-3 Kaministiquia River Lake Sturgeon Study Completed Monitoring Initiative (2004 - 2013) MNR $33,000/year SM-FWP-4 Current River Walleye Assessment Completed Monitoring Initiative (1991 - 1993, 2010 - 2012) MNR $10,000/year SM-FWH-1 Fish Habitat Classification and Assessment Completed Monitoring Initiative (2012) EC/MNR $30,000 SM-FWH-2 Northern Wood Preservers Alternative Remediation Concept (NOWPARC) Fish Community Comparison Completed Monitoring Initiative (2005 - 2006) MNR/DFO NA 4 Status of Fish Habitat The delisting criteria for fish habitat, as developed by the RAP team in consultation with the local Public Advisory Committee, are itemized below. The rationale for each criterion, the activities undertaken to reach a solution, and the status of each in terms of its completeness and effectiveness are documented. Finally, other outstanding fish habitat issues are discussed. 10 Status of Fish Populations and Habitat in Thunder Bay 4.1 Delisting Criteria: A Review This beneficial use will no longer be impaired when the following habitat-related projects from the Thunder Bay Stage 2 RAP Report (2004) have been completed, evaluated for effectiveness, and areas support diverse self-sustaining biological communities: 1. Alleviation of water quality barriers to fish migration in the Kaministiquia River o Rationale: Depressed oxygen levels had created intermittent barriers to fish movement between the harbour and unimpaired habitat in the upper reaches of the river due to high BOD loadings from the Bowater pulp and paper mill. o Activities: Strict environmental regulations were applied to limit effluent discharges. Secondary treatment of effluent was initiated at Bowater`s kraft (1991) and newsprint (1995) mills. Another downstream industrial source of organic wastes was eliminated through plant closure (Ogilvie Mills Ltd.). Monitoring of water quality through this period and in recent years has revealed a dramatic improvement in dissolved oxygen levels. o Status: Effective - water quality barrier eliminated. 2. Re-vegetation projects in McVicar Creek and McKellar River o Rationale: Construction associated with two habitat improvement projects (discussed below) resulted in loss of vegetation along embankments and adjacent areas. o Activities: Over 4000 indigenous trees and shrubs were planted on areas disturbed by construction on Mission Island near the mouth of the McKellar River and aquatic macrophye growth was established within the embayments (Lee 1995). At the McVicar Creek site, the road embankment was seeded with grasses and 2300 mixed shrubs and deciduous and coniferous trees (all indigenous to the area) were planted in 1993 and 1994 (Geiling 1995b). o Status: Effective - shrubbery has anchored soils and provided bank stabilization along with food and cover for wildlife. 3. Habitat improvements associated with the creation of Sanctuary Island at the mouth of McVicar Creek o Rationale: An overpass constructed in 1985 resulted in erosion of embankments, restricted fish passage, and caused the infilling of a small wetland area. o Activities: Bank stabilization, substrate enhancement, and terracing of the lower portion of the road embankment were completed 1992 to restore fisheries habitat (Geiling 1995b). A crescent shaped island was built in 1993 just south of the creek mouth to recreate nearshore nursery habitat and to encourage the re-establishment of a historic wetland site (Geiling 1995c). Eight rock shoals were installed underwater in the lee of the island to provide cover, shelter, and habitat diversity. o Status: Effective - anecdotal reports following construction indicated some positive change, as confirmed by more recent MNRF electrofishing sampling. 11 Status of Fish Populations and Habitat in Thunder Bay 4. Habitat remediation on McKellar River o Rationale: Decades of dredging for commercial ship traffic produced a straight, deep channel and a shoreline partly armoured with steel sheet piling and concrete. Most of the shallow littoral zone has been eliminated leaving little in the way of habitat productivity or diversity. This demonstration project was to be a small step in correcting this. o Activities: Two shallow embayments were created in 1994 near the mouth of the McKellar River adjacent to the Mission Marsh Conservation Area in order to increase the littoral zone and provide an additional three hectares of wetland habitat. Diverse habitats were provided with detailed bottom grading, gravel shoals, sand spits, a sand bluff for nesting bank swallows, and shallow woodland pools for amphibians. o Status: Effective - monitoring in the first two seasons after construction has indicated that a number of fish, waterfowl, songbirds, and mammals have made extensive use of the new habitat. Benthic organisms have also colonized the embayments. A comparative fish study carried out in 2005-06 found that fish species abundance was notably high at this site when compared to other contemporary sites and with historical data (Parker et al. 2008). 5. Rehabilitation of walleye spawning habitat at Current River Estuary o Rationale: The mouth of the Current River provides spawning and nursery habitat for one of the few remaining, naturally reproducing walleye stocks in Lake Superior. Dredging for a small craft harbour in 1984 along with other earlier road and rail construction destroyed a portion of this habitat. o Activities: Artificial extensions to walleye spawning areas were created at three sites in 1991, doubling the area of known spawning habitat (Geiling 1995a). Early monitoring indicated some use of these new sites (Geiling et al. 1996). o Status: Ineffective - the number of spawning walleye have declined at this site from 1485 (1993) to 364 (2010) based on mark‐recapture population assessments (Bobrowicz 2011). A recent substrate mapping project has revealed that the artificial spawning substrate is not being used (S. Finucan, MNRF, pers. comm.). 6. Improving salmonid access to the upper reaches of the Current River o Rationale: The Current River has approximately 50 km of potential spawning and nursery habitat available to rainbow trout, however passage was blocked by a dam situated approximately 600 m upstream from the mouth of the river. Providing access was expected to result in a self-sustaining rainbow trout population within the river. o Activities: A fish ladder was completed in 1992 and resting pools excavated below in 1995. Spawning adult rainbow trout were transferred upstream over a four year period to help establish the population. o Status: Ineffective - objectives have not been realized. 7. Implement the Slate River Watershed Management Plan o Rationale: Nutrient enrichment and erosion within the Slate River tributary have resulted in the physical degradation of benthic habitat downstream in the Kaministiquia River. A 12 Status of Fish Populations and Habitat in Thunder Bay o o Watershed Management Plan completed in 1998 recommends improved water management practices in order to reduce the impact of organic enrichment, turbidity, and sedimentation on the stability of benthic habitat and levels of productivity in this portion of the AOC. Activities: A Slate River Watershed Assessment Report was completed in 2008 with a focus on water quality issues (Maki and Grinstead 2008). Status: Incomplete - the Lakehead Region Conservation Authority has determined that full implementation of this plan is not warranted as many of the actions recommended in the plan have now been accomplished. 8. Monitoring to support lake sturgeon rehabilitation strategy o Rationale: A rehabilitation plan for lake sturgeon was developed by a binational technical committee to maintain, enhance and rehabilitate self-sustaining populations in Lake Superior (Auer 2003). The monitoring of the Kaministiquia River population was an opportunity to advance our knowledge of this species within the AOC. o Activities: Studies have been conducted annually from 2004 to 2013 to determine sturgeon movements and spawning success under different water flows and levels within the Kasministiquia River in order to identify conditions necessary for their successful reproduction. o Status: Effective - ten years of study have resulted in advancements to this knowledge base and a new methodology for estimating the critical reproductive periods for this species (Friday 2014). In addition to the Stage 2 RAP projects, the following should also be completed: 9. Implement plan for shoreline naturalization within the Thunder Bay AOC o Rationale: Urban and industrial development and cottaging has disturbed vast areas of shoreline within the AOC, as described in the Stage 1 RAP. Much of the shoreline within the harbour has been drained and filled, including wetlands. A naturalization plan has been proposed that would include a strategy for both municipally and privately owned land, as well as a series of demonstration projects that will generate public awareness and promote the effectiveness of this type of project. o Activities: While a number of shoreline naturalization projects have been carried out (e.g., Current River estuary, island creation at mouth of McVicars Creek, McKeller River embayments, the redesigned Wilson Street headland on Thunder Bay’s waterfront), an overall plan for the naturalization of shorelines within the AOC has not been produced. o Status: Incomplete - discussions around a larger Thunder Bay-wide naturalization plan have yet to take place. 13 Status of Fish Populations and Habitat in Thunder Bay 10. Remaining and created wetlands are protected from further degradation through existing environmental legislation, with provincial standards used to inventory and classify wetlands within the Thunder Bay AOC o Rationale: There has been substantial disturbance to shorelines within the AOC and further loss of wetlands is unacceptable. o Activities: Provincial standards exist for wetland classification purposes (Harris et al. 1996). Shoreline wetlands are currently protected under Section 35 of the federal Fisheries Act, although recent alterations to this act (2013) have resulted in what some consider to be a relaxation of protection of fish habitat, particularly where undeveloped fisheries exist (Hutchings and Post 2013). o Status: Effective – providing legislation is fully enforced, as the waters in the Thunder Bay AOC support a viable commercial, recreational, and Aboriginal fishery. 11. Provide unrestricted access to critical spawning habitat by providing adequate flow in the Kaministiquia River o Rationale: During the Kaministiquia River Water Management Planning process, MNRF identified two issues concerning water management practices at Kakabeka Falls. The first was access of adult sturgeon to their historical spawning site at the base of Kakabeka Falls; the second was stranding of adults between the falls and the generating station. o Activities: Studies have been conducted annually from 2004 to 2013 to determine sturgeon movements and spawning success under different water flows and levels within the Kasministiquia River in order to determine conditions necessary for their successful reproduction (access, egg deposition, incubation, hatch, and larval drift). o Status: Incomplete - the required water flows have been determined, however changes have not yet been made to the Kaministiquia River Water Management Plan to ensure they will be provided. 12. Ensure that native fish populations are not negatively affected by industrial water-use practices, including water intake and discharge o Rationale: Industrial water use practices have historically affected water quality and water temperature and have been responsible for the loss of fish production within the AOC. o Activities: Provincial environmental legislation was strengthened in the early 1990’s to include the Municipal-Industrial Strategy for Abatement (MISA) regulations introduced under the Environmental Protection Act to address water discharge issues associated with nine industrial sectors. o Status: Effective - providing legislation is fully enforced. 14 Status of Fish Populations and Habitat in Thunder Bay 4.2 Outstanding habitat issues The review above indicates that while most of the remediation projects have been completed and have demonstrated some degree of effectiveness, there is still some work to do. Three projects are incomplete, although the need to proceed is in question for the latter two: o o o Provide unrestricted access to critical spawning habitat by providing adequate flow in the Kaministiquia River Implement the Slate River Watershed Management Plan Implement plan for shoreline naturalization within the Thunder Bay AOC Two projects have proven to be ineffective and may require further action. These are discussed further as part of the fish population review: o o Rehabilitation of walleye spawning habitat at Current River estuary Improving salmonid access to the upper reaches of the Current River In addition, there are still concerns with point source and non-point sources of pollution in the AOC, which all have fish habitat implications. Stormwater has been identified as a non-point source that must be dealt with. Stormwater impact assessments have been made on three water systems that discharge into Lake Superior within the AOC: McVicar Creek, Lower Neebing River, and Lyons/Third Avenue channels. The City of Thunder Bay is currently finalizing its Stormwater Master Plan which should include mitigation strategies to address these concerns. A second area of concern is the site of the former Cascades Fine Paper property (Thunder Bay North Harbour) with 22 ha of sediments comprised of waste wood products that are substantially elevated in mercury and other contaminants (Grapentine 2011). In addition, areas east of the Mission and McKellar deltic islands and the Smurfit-Stone Container Canada Inc. site (formerly Thunder Bay Packaging, located north of the break wall outside of the Thunder Bay Harbour) have sediment contamination issues. 5 Status of Fish Populations The status of fish populations in the Thunder Bay AOC are to be judged under prescribed delisting criteria, which have been guided by the Fish Community Objectives for Lake Superior (Horns et al. 2003) and individual species restoration plans. The fish community and individual fish species are evaluated against these criteria and discussed below. 15 Status of Fish Populations and Habitat in Thunder Bay 5.1 Delisting Criteria Fish populations will no longer be impaired when the fish community within the AOC has the following characteristics, as observed by the MNRF Fish Community Index Netting (FCIN) program. The fish community within the Thunder Bay AOC should be similar to nearshore (0–80 m deep) fish communities adjacent to the AOC for a minimum of three consecutive years, as measured by the relative abundance (Catch Per Unit Effort) and species composition of the fish community. Also, the nearshore fish community should be dominated by self-sustaining populations of native species showing the following characteristics: Lake Trout • The mean age of lake trout is greater than eight years. • The length at age of seven-year old lake trout caught in the FCIN or harvested by the commercial fishery is stable and greater than 430 mm. • The FCIN and/or commercial catch is dominated by mature fish and many age classes. Lake Whitefish • Population capable of supporting a commercial fishery with sustainable yields that do not exceed 0.51 kg/ha/yr (Busiahn 1990) • Maximum total annual mortality does not exceed 60-65%. • Average age in the catch should be two years older than the age at which 50% of the population matures. Lake Sturgeon, Walleye and Brook Trout The overall understanding of the population dynamics of these native species within Thunder Bay is limited; therefore it is difficult to establish population criteria. Efforts are currently underway to better understand these species and their habitat use within Thunder Bay and its tributaries. As a result, criteria that reflect lake sturgeon, walleye, and brook trout populations are covered under the loss of habitat delisting criteria. 5.2 Fish Community Thunder Bay supports a diverse fish community with 55 species confirmed from within the harbour area (Foster 2012; Appendix 1). However, the introduction and invasion of exotic species over the past 130 years or more have altered the natural ecosystem. Over one quarter of the fish species contributing to the fish community are now non-native. 16 Status of Fish Populations and Habitat in Thunder Bay The delisting criteria for fish communities require that species composition and relative abundance be similar in areas within and adjacent to the AOC. This was determined by examining catches collected over a six year period (2009-2014) as part of MNRFs Fish Community Index Netting (FCIN) program. The nearshore fish community (0-80 m deep) of the AOC was found to be more diverse than those areas adjacent to it. A total of 16 species were observed in FCIN catches within the AOC, while 11 were found in outside areas (Table 3). Four of the additional species found within the AOC were non-native to Lake Superior. The catch per unit effort of fish (all species) is identical inside and outside of the AOC (22.9 versus 23.1 fish/km). However, there is a difference between the contributions of individual species (Figure 3). The catch outside of the AOC is dominated by lake trout and lake herring (cisco), with lake whitefish and bloater being other important components. Longnose sucker is the dominant species within the AOC, with lake herring (cisco), lake whitefish and lake trout also contributing significantly to the catch. While differences exist between the fish community within and adjacent to the AOC, these would not in any way suggest impairment to the populations within the AOC. Both the increased diversity within the AOC (a good thing) and variation in species abundance is most likely attributable to difference in physical habitat that exists within these areas. Table 3: Comparison of nearshore fish species occurrence both within and immediately outside of the AOC based on FCIN catches. Species non-native to Lake Superior are indicated with an asterisk. Species Lake sturgeon Alewife* Chinook salmon* Lake trout Lake whitefish Cisco Bloater Kiyi Shortjaw cisco Round whitefish Rainbow smelt* Longnose sucker White sucker Burbot Rock bass* Walleye Ruffe* Sculpins Occurrence Inside AOC Outside AOC x x x x x x x x x x x x x x x x x x x x x x x x x x x 17 Status of Fish Populations and Habitat in Thunder Bay 80 70 Catch per Unit Effort (#/km) 60 50 40 30 20 10 Burbot White sucker Longnose sucker Rainbow smelt Round whitefish Shortjaw cisco Kiyi Bloater Cisco Lake whitefish Lake trout 0 Figure 3: Relative abundance (catch per unit effort) of nearshore fish species sampled inside (blue bars) and outside (red bars) of the AOC. Data represents means from FCIN averaged over a six year period (2009-2014), omitting rare species. 5.3 Lake Trout The delisting criteria include three specific measures of lake trout health. The first of these is a measure of the longevity of the population, described in terms of mean age. An index value of 8 years represents the minimum acceptable. The mean age of lake trout in FCIN samples collected from 2009 to 2013 within the AOC ranged from 12.3 to 14.1 years, with an average of 13.4 years, far exceeding the index value (Table 4). The second criterion examines the growth rate of lake trout which is commonly expressed as size at a given age (Figure 4). The total length at age seven is used as a growth standard in Lake Superior with 430 mm used as baseline value (Hansen 1996). It was found that the sample size within the AOC alone was too small to examine this metric (less than 5 fish in all but one year) so fish both within and immediately outside of the AOC were combined for this analysis. Results show that lake trout were on average 433 mm total length at age seven. There appears to be a slight increase in growth through the five year period (Table 4), but this difference is not statistically significant. The last measure of health is related to lake trout recruitment and maturity. The age structure of lake trout sampled inside and outside of the AOC is near identical (Figure 5), which is as expected as the population is common within the Bay. Thirty five continuous age classes of lake trout have been 18 Status of Fish Populations and Habitat in Thunder Bay observed in FCIN samples collected from 2009 to 2013. Numerous older fish are seen up to age 35 and two fish have reached 46 years of age. This is a characteristic of a healthy, robust population that is experiencing regular annual recruitment. On average, 91.5% of the fish in the FCIN samples are mature, as are 100% of the fish in the commercial harvest. All delisting criteria have been satisfied for lake trout populations within the AOC. Table 4: Statistics related to delisting criteria for lake trout from annual FCIN sampling (2009-2014) within the AOC. Values for Length at Age 7 include samples from area adjacent to AOC to provide adequate sample sizes. Year 2009 2010 2011 2012 2013 All Mean Age (yr) Length at Age 7 (mm) Percent mature 13.4 406 99.1 14.1 424 92.2 13.5 415 97.1 13.2 465 85.0 12.3 458 93.8 13.4 433 91.5 Number of Age Classes 19 16 18 17 19 18 800 700 Total Length (mm) 600 500 400 300 200 100 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 Age (years) Figure 4: Lake trout mean total length at age from FCIN samples 2009-2014. 19 Status of Fish Populations and Habitat in Thunder Bay 10 Outside AOC Inside AOC 9 8 Percent of Catch 7 6 5 4 3 2 1 0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 Age (years) Figure 5: Age frequency histogram for lake trout sampled inside (red bars) and outside (blue bars) of the AOC in FCIN (2009-2013). 5.4 Lake Whitefish A commercial fishery for lake whitefish exists within the waters of Thunder Bay that has been sustained over many decades. Traditionally, it has supported the third highest harvest of lake whitefish from all areas of the lake (Ebener et al. 2008). Portions of three quota management areas (QMA) extend into the AOC: Zone 1, 2, and 4. Lake whitefish yields within these zones over the period of 2009 to 2013 averaged 0.21, 0.04, and 0.02 kg/ha/yr, respectively. These are well below the 0.51 kg/ha/yr limit that has been identified within the fish community objectives for Lake Superior (Busiahn 1990). Total annual mortality is another measure of lake whitefish health. In the lake whitefish commercial catch, annual mortality averaged 37% from 2009 to 2012 (Figure 6). Mortality measured from the FCIN catch from 2009 to 2014 was lower still, commonly less than 20%. Both values are less than the value of 60-65% which has been deemed the maximum acceptable for lake whitefish. 20 Status of Fish Populations and Habitat in Thunder Bay The last health index is related to turnover time in the population (Abrosov 1969). It is suggested that the mean age of the commercial catch should exceed the age of 50% maturity by at least two years. The mean age of maturity calculated from FCIN samples from 2009 to 2014 was 4.6 for males and 5.5 for females. The mean age in the commercial catch from 2009 to 2012 was 12.7 yr, which would allow many spawning opportunities (Figure 7). All delisting criteria have been satisfied for lake whitefish populations within the AOC. 50 Commercial Catch FCIN Total Annual Mortality 40 30 20 10 0 2009 2010 2011 2012 2013 2014 Year Figure 6: Total annual mortality of lake whitefish as indicated from commercial catch and fish community index nets. Mortality was calculated through linear regression of the descending limb of the catch curve from modal age onward where sample sizes exceeded four fish per age class (Ricker 1975). 21 Status of Fish Populations and Habitat in Thunder Bay 16% 14% Percent of obs 11% 9% 7% 5% 2% 0% 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 AGE Figure 7: Lake whitefish age structure from commercial catch (2009-2012). 5.5 Lake Sturgeon, Walleye and Brook Trout These species are not sampled as part of any regular agency monitoring program and their population dynamics are not well-understood in the AOC. As a result, it has been proposed that loss of habitat delisting criteria be used as a surrogate for these species. 5.5.1 Lake Sturgeon Three habitat-related projects have been completed that are directly related to lake sturgeon rehabilitation in Thunder Bay: Alleviation of water quality barriers to fish migration in the Kaministiquia River (FWH-7) Monitoring to support lake sturgeon rehabilitation strategy (FWP-1) 22 Status of Fish Populations and Habitat in Thunder Bay Provide unrestricted access to critical spawning habitat by providing adequate flow in the Kaministiquia River (SM-FWP-3) Lake sturgeon are listed as “threatened” under Ontario’s Endangered Species Act and their habitats are awarded special protection. The natural flow regimes of many rivers flowing into Lake Superior that once supported spawning lake sturgeon have been radically altered by construction of hydroelectric facilities, along with land use activities (Auer 2003). Where this has occurred, the lake sturgeon rehabilitation plan for Lake Superior recommends establishing relicensing criteria for the hydroelectric facility to ensure run-of-river flows and appropriate annual water regime for lake sturgeon reproduction and survival (Auer 2003). In the recent past, lake sturgeon migration to and from their historic spawning site at the base of Kakabeka Falls was impeded by a water quality barrier in the lower river and by low water flows in the upper river. Stranding of adults between the falls and the hydroelectric generating station was also an occurrence. These issues have been partially resolved. Secondary treatment of effluent at the Bowater (Resolute) kraft and newsprint mill has eliminated the water quality barrier downstream. A better understanding of lake sturgeon spawning requirements has been gleaned through ten years of monitoring the population and the timing and quantity of water flow necessary to meet the needs of this species in the upper river during their spawning period have now been documented (M. Friday, MNRF, pers. comm.). However, these requirements have yet to be formally translated into operational changes in a revised Water Management Plan for the Kaministiquia River. The current plan, due for renewal in 2015, has been extended for two years and discussions have yet to take place on this issue (Emily Hawkins, MNRF, pers.comm.). Unlike most other populations in the Great Lakes, the individuals in this population may be year-round river residents (Friday and Chase 2005). High genetic differentiation from other Great Lakes spawning populations suggests that few migrants enter the river for spawning (Welsh et al. 2008). It was estimated in a 2001 mark-recapture study that there was an adult population of 196 (144-304) individuals residing in the lower river (M. Friday, MNRF, unpublished data). The lake sturgeon rehabilitation plan for Lake Superior suggests there should be at least 1,500 mature, spawning adults capable of ascending the river to spawn, even though not all of them spawn each year (Auer 2003). We are far from this restoration goal. Many changes have been made to aid the recovery of this population. Angling harvest restrictions implemented in 2009 ensure that fishing mortality is no longer a threat. Water quality has been improved within the river and some changes have been made to the flow regime to improve access to and from lake sturgeon spawning grounds. A recent genetic study has indicated that reproduction has been successful at this site (Welsh et al. 2014). However, until there are signs that the population is responding to these habitat improvements with an increase in adult fish, we cannot consider this population rehabilitated. A mark-recapture study planned for 2015 will provide an updated population estimate which may shed more light on this issue. 23 Status of Fish Populations and Habitat in Thunder Bay 5.5.2 Walleye Four habitat-related projects have been completed that are directly related to walleye rehabilitation in Thunder Bay: Alleviation of water quality barriers to fish migration in the Kaministiquia River (FWH-7) Rehabilitation of walleye spawning habitat at Current River estuary (FWH-1) Kaminisiquia River walleye radio telemetry project (SM-FWP-2) Current River walleye assessment (SM-FWP-4) Thunder Bay supports one of the few remaining walleye populations in Lake Superior (Hoff 2002). A known spawning site for walleye is the mouth of the Current River, which had been degraded through time by railway and shipping-related development and through dredging as part of the construction of federal docks. Additional spawning beds were constructed in 1991 to compensate for habitat loss at this site and monitoring at the time indicated some degree of success, with spawning occurring on the new sites (Geiling et al. 1996). This use has not continued. An underwater survey was undertaken at the mouth of the Current River in 2014 to map the substrate in relation to water depth and velocity (S. Finucan, MNRF, pers. comm). Egg mats were deployed and revealed that walleye spawned in the two eastern side channels but did not make use of the artificial spawning beds. Coarse substrate at the spawning sites was found to be embedded with fines and appeared less than ideal for walleye. Some of this fine material may have accumulated during construction of the fish ladder and resting pools for rainbow trout that had been constructed 600 m upstream in the early 1990s. Other habitat issues may be at play. In April 2010, it was noted that the operation of the Current River hydroelectric facility was not conducive to walleye spawning, with flows reduced at night in order to store water for daytime hydro generation (Bobrowicz 2011). On at least one occasion, flow at the mouth of the river ceased altogether, stranding fish and presumably leaving eggs exposed. The Water Management Plan for the facility should be adjusted to ensure that adequate flows for spawning walleye are available at this critical time of the year. Periodic assessments have been carried out to determine the size of the walleye spawning population. In the years immediately following the construction of the Current River artificial spawning beds, the walleye spawning population ranged from about 1100 to 1500 fish (Geiling et al. 1996). The most recent estimate (2010) indicates that less than 400 fish are now using this site (Bobrowicz 2011). It is unknown if this represents a reduction in overall population size or a shift in preferred spawning locations. Telemetry projects have recently been undertaken (2010-2012) to help answer this question. Transmitters were implanted in fish captured in both the Kaministiquia River and the mouth of the Current River in the spring of the year (E. Berglund, MNRF, unpublished report). Data from this study, although preliminary, suggests that the Current River may now be more of a staging area, with most 24 Status of Fish Populations and Habitat in Thunder Bay walleye moving to the Kaministiquia River during the peak spawning period. This could have also been the case in the past, with the large number of fish recorded in this area simply staging prior to spawning while feeding on the abundant rainbow smelt. As part of this study, it was found that nearly 20% of the walleye that were tagged at the mouth of the Current River in the spring of 2010 were caught by anglers in the Kaministiquia River. This raises a red flag as it suggests that the exploitation rate of this population may be quite high. A creel census was carried out on the river in 2012 and a conservative estimate of the annual harvest was at least 1000 fish (E. Berglund, MNRF, unpublished data). This represents a high rate of fishing mortality that must be reduced, as a continuation of this pressure is known to impede the rate of recovery of degraded fish populations (Hutchings 2000). The Lake Superior rehabilitation plan for walleye cites a goal of 5000 spawning adults in Thunder Bay (Hoff 2002). Current information suggests that this target is far from being met, and in fact, a decline in numbers may have occurred over the past two decades. 5.5.3 Brook Trout There were no habitat-related Stage 2 projects directly related to brook trout, but other habitat improvements may have had indirect benefits to this species, such as: removal of the water quality barrier in the Kaministiquia River (FWH-7) habitat rehabilitation at McVicar Creek mouth (FWH-3) shoreline habitat improvements at McKellar River (FWH-5). These projects have all been completed and have shown varying degrees of success. It is expected that each of these may have provided some improvement to habitat for brook trout within these rivers. The City of Thunder Bay’s updated Stormwater Master Plan, when implemented, should provide improvements to water quality that would benefit brook trout within the urban streams. In addition to the Stage 2 projects, the George Creek restoration was completed in 2013. Through a community partnership a degraded brook trout tributary of the Current River was restored through the creation of pools and riffles and habitat features to improve nursery areas that were previously destroyed. The riparian zone was repopulated with native trees, shrubs, and herbaceous plants that will increase shade and improve the productivity of the creek. However, one of the projects of the Stage 2 RAP may actually have been detrimental to this brook trout population. In 1992 a fish ladder was constructed on the Current River immediately below Boulevard Lake to provide access for migratory salmonids to the upper 50 km of river. While this would have provided a range expansion for the exotic rainbow trout, as planned, it would have negatively affected the native brook trout population. Through competition for food and space, rainbow trout have been shown to severely reduce the abundance and distribution of brook trout in shared watersheds (Larson 25 Status of Fish Populations and Habitat in Thunder Bay and Moore 1985; Blanchet et al. 2007). In some locations, the removal of rainbow trout from streams has been used as a management tool to recover native brook trout populations (Moore et al. 1983; Kulp and Moore 2000). The fish ladder has failed to fulfill its purpose through design flaws and water use conflicts. With respect to native brook trout, this failure may be a good thing. No monitoring or assessment of brook trout populations in the Thunder Bay AOC has been done and the current status of these populations cannot be concluded. 6 Conclusions 6.1 Fish Habitat The fish habitat delisting criteria and the status of each for the Thunder Bay AOC are summarized in Table 5. There have been vast improvements made to fish habitat within the Thunder Bay AOC over the past 25 years. Water quality barriers have been eliminated, contaminant sediments removed, and damaged shorelines and spawning areas have been reconstructed. However, there is still degraded fish habitat within the AOC. The adverse effects of stormwater runoff must be mitigated within Thunder Bay watersheds as the high levels of nutrients and metals contaminate the living space of fish and other aquatic biota residing in these streams. The City of Thunder Bay has completed a stormwater impact assessment on three primary watersheds and is in the process of implementing its Stormwater Master Plan which is expected to address these concerns. The Contaminated Sediment Management Area within the North Harbour area is known to provide nursery, foraging and overwintering habitat for a number of different fish species (Foster 2012). The rehabilitation of bare pulp substrates at this location will potentially increase the habitat values for these fish. A management plan is being developed to remediate this area. Two management/rehabilitation plans (Slate River Watershed Management; shoreline naturalization) that are part of the delisting criteria have not been implemented, although the need to proceed with these is in question. In addition, two habitat restoration projects on the Current River have proven to be ineffective to some degree (spawning bed creation; fish ladder for salmonid access). Also, unrestricted access to critical spawning habitat for lake sturgeon in the Kaministiquia River has not yet been guaranteed. 26 Status of Fish Populations and Habitat in Thunder Bay Table 5: Summary table illustrating status of fish habitat delisting criteria within Thunder Bay AOC. A green check mark indicates that work has been completed to address the problem with effective results. A yellow check mark indicates that the project has been completed, but the results are not satisfactory. A red check mark indicates a lack of progress on this issue. Criteria Status 4 4 1 Alleviation of water quality barriers to fish migration in the Kaministiquia River 2 Re-vegetation projects in McVicar Creek and McKellar River 3 Habitat improvements associated with the creation of Sanctuary Island at the mouth of McVicar Creek 4 4 Habitat remediation on McKellar River 5 Rehabilitation of walleye spawning habitat at Current River Estuary 6 Improving salmonid access to the upper reaches of the Current River 7 Implement the Slate River Watershed Management Plan 8 Monitoring to support lake sturgeon rehabilitation strategy 9 Implement plan for shoreline naturalization within the Thunder Bay AOC 4 4 4 8 4 8 Remaining and created wetlands are protected from further degradation through 10 existing environmental legislation, with provincial standards used to inventory and classify wetlands within the Thunder Bay AOC 4 11 Provide unrestricted access to critical spawning habitat by providing adequate flow in the Kaministiquia River 4 12 Ensure that native fish populations are not negatively affected by industrial wateruse practices, including water intake and discharge 4 6.2 Fish Populations The status of fish populations within the Thunder Bay AOC is summarized in Table 6. The delisting criteria for lake trout and lake whitefish involve quantifiable metrics related to, growth, maturation and mortality. When measured against these, both species can be considered unimpaired in the Thunder Bay AOC. The overall fish community of nearshore waters is similar inside and outside the AOC and can also be considered unimpaired. For three ancillary species (lake sturgeon, walleye, and brook trout) quantifiable metrics do not exist and rehabilitation of their habitat is to be used as a surrogate for delisting. For lake sturgeon, water quality enhancements within the Kaministiquia River and an angler harvest restriction are viewed as positive actions. However, early summer water flows in the upper river have proven to be inadequate to promote a high level of spawning success. The Kaministiquia River Water Management Plan should be amended to ensure this is corrected, as directed by the lake sturgeon 27 Status of Fish Populations and Habitat in Thunder Bay rehabilitation plan for Lake Superior (Auer 2003). This remains the last known impediment to the lake sturgeon population within the AOC. Once corrected, the population should slowly rebuild to the carrying capacity of the system, which would be expected to take a great number of years to accomplish. Walleye in the AOC have shown no improvements in abundance, in spite of water quality and spawning habitat improvements. The spawning bed enhancement at the mouth of the Current River has shown only limited success and controls over water flow may be partially at fault. The Water Management Plan for the Current River should be adjusted to ensure that adequate flows occur at this critical time of the year. However, recent telemetry studies have provided a new understanding of walleye use of this area. It appears that at least in recent years, walleye may simply be staging and feeding at this site prior to moving to the Kaministiquia River to spawn. If further studies confirm this, additional improvements of spawning substrate and changes to flow regimes on the Current River may not be so important for this species, although lack of sufficient flows may continue to compromise spawning salmonids. Angling activity directed at walleye appears to be increasing within the AOC. A creel census on the Kaministiquia River in 2012 revealed an annual harvest of ~1000 fish. This represents a high rate of exploitation on this residual population. Immediate steps should be taken to reduce this source of mortality, which would hasten the recovery of this population. Regular monitoring of the walleye population should be carried out through mark-recapture studies to determine changes in abundance. A population approaching 5000 adult fish would be considered rehabilitated (Hoff 2002), although it could take many years to achieve this. Brook trout habitat continues to be compromised through current stormwater management practices. Improvements to their habitat should occur following the implementation of Thunder Bay’s Stormwater Master Plan. Table 6: Overview of fish population status within the Thunder Bay AOC. A green check mark indicates that the delisting criteria are completely satisfied; a yellow check mark indicates that habitat issues for the species persist but are soon to be rectified; a red check mark indicates that the population remains depressed for a variety of reasons. Status Fish Community Lake Trout Lake Whitefish Lake Sturgeon Walleye Brook Trout 4 4 4 4 8 4 28 Status of Fish Populations and Habitat in Thunder Bay 7 Literature Cited Abrosov, V.N. 1969. Determination of commercial turnover in natural bodies of water. Translations of Problems of Ichthyology. Am. 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Thunder Bay, Ont. Field Guide FG‐01. 74 pp. + Append. Hoff, M. H. [ED.]. 2002. A rehabilitation plan for walleye populations and habitats in Lake Superior. Great Lakes Fish. Comm. Misc. Pub. 2003-01. Horns, W.H., C.R. Bronte, T.R. Busiahn, M.P. Ebener, R.L. Eshenroder, T. Gorenflo, N. Kmiecik, W. Mattes, J.W. Peck, M. Petzold, D.R. Schreiner. 2003. Fish-community objectives for Lake Superior. Great Lakes Fish. Comm. Spec. Pub. 03-01. 78 p. Hutchings, J.A. 2000. Collapse and recovery of marine fishes. Nature 406: 882–885. Hutchings, J. A., and J.R. Post. 2013. Gutting Canada's Fisheries Act: No Fishery, No Fish Habitat Protection. Fisheries 38: 497–501. 30 Status of Fish Populations and Habitat in Thunder Bay Kulp, M.A. and S.E. Moore. 2000. Multiple electrofishing removals for eliminating rainbow trout in a small southern Appalachian Stream. North American Journal of Fisheries Management 20:259-266. Larson. G. L., and S. E. Moore. 1985. Encroachment of exotic rainbow trout into stream populations of native brook trout in the southern Appalachian Mountains. Transactions of American Fisheries Society 114:195-203. Lawrie, A. H., and J. F. Rahrer. 1972. Lake Superior: effects of exploitation and introductions on the salmonid community. Journal of the Fisheries Research Board of Canada 29:765–776. Lee, P.F. 1995. Aquatic macrophyte establishment in McKellar River embayments at Thunder Bay, Ontario., pages 179-183. In J.R.M. Kelso and J.H. Hartig [editors]. 1995. Methods of modifying habitat to benefit the Great Lakes ecosystem. CISTI Occas. Pap. 1: 294 pp. Maki, C, and J. Grinstead. 2008. Slate River Watershed Assessment Report. Lakehead Region Conservation Authority. 101p. Moore, S. E., R. L. Ridley, and G. L. Larson. 1983. Standing crops of brook trout concurrent with removal of rainbow trout from selected streams in Great Smoky Mountains National Park. North American Journal of Fisheries Management 3:72- 80 Nicholson, A. 2013. Thunder Bay Remedial Action Plan Update 2009-2012. Lakehead University. 38 p. Parker, S., P.A, Addison, K.J. MacIntosh and G.R Garach. 2008. Fish Community Comparison Between Nearshore Remediation Areas of the Northern Wood Preservers Facility and Four Nearshore Areas within Thunder Bay Harbour in 2004 and 2006. Northern Wood Preservers Alternative Remediation Concept (NOWPARC). Ontario Ministry of Natural Resources, Upper Great Lakes Management Unit, Lake Superior, Thunder Bay, Ontario. 52 p. Ricker, W. E. 1975. Computation and interpretation of biological statistics of fish populations. Fisheries Research Board of Canada, Bulletin 191. Schloesser, J., G. Czypinski, and H. Quinlan. 2012. Early detection of invasive fishes in Lake Superior: St. Louis River, Upper St. Marys River, and Thunder Bay assessments, 2011. U.S. Fish and Wildlife Service, Ashland Fish and Wildlife Conservation Office, Technical Report No. 03. Ashland, WI. 27 pp. Sutton, J.A. 1975. Bottom fauna of dredge soil deposits in Thunder Bay. Unpublished Manuscript. Ontario Ministry of the Environment. 34 p. Thunder Bay RAP Team. 1991. Thunder Bay Area of Concern Remedial Action Plan Stage 1: Environmental Conditions and Problem Definition. 109 pp. 31 Status of Fish Populations and Habitat in Thunder Bay Vander Wal, J., K. Cullis, M. Chase, P. Morash and T. Cano. 2004. Thunder Bay Remedial Action Plan – Stage 2: Remedial Strategies for Ecosystem Restoration. 74pp. plus appendices. Welsh A, Hill T, Quinlan H, Robinson C, May B. 2008. Genetic assessment of lake sturgeon population structure in the Laurentian Great Lakes. N. Am. J. Fish. Manag. 28:572–591 Welsh, A.B., Baerwald, M.R., Friday, M., and May, B. 2014. The effect of multiple spawning events on cohort genetic diversity. Environmental Biology of Fishes DOI 10.1007/s10641-014-0309-9. 32 Status of Fish Populations and Habitat in Thunder Bay 8 Appendix l: Fishes of Thunder Bay Harbour Area List compiled by Foster (2012) from multiple sources. Species marked with an * are not native to Lake Superior. Scientific Name Common Name ______________________________________________________________________________ Lampetra lamottei American brook lamprey Petromyon marinus Sea lamprey* Ichthyomyzon unicuspis Silver lamprey Acipenser fluvescens Lake sturgeon Alosa pseudoharengus Alewife* Oncorhynchus gorbuscha Pink salmon* Oncorhynchus kisutch Coho salmon* Oncorhynchus tshawytscha Chinook salmon Oncorhynchus mykiss Rainbow trout* Salmo trutta Brown trout* Salvelinus fontinalis Brook trout Salveljnus namaycush Lake trout Coregonus artedii Lake herring Coregonus clupeaformis Lake whitefish Apeltes quadracus Gizzard shad* Prosopium cylindraceum Round whitefish Osmerus mordax Rainbow smelt* Umbra limi Central mudminnow Esox lucius Northern pike Chrosomus eos Northern redbelly dace Chrosomus neogaeus Finescale dace Cyprinus carpio Common carp* Notropis atherinoides Emerald shiner Notropis cornutus Common shiner Notropis heterolepis Blacknose shiner Notropis hudsonius Spottail shiner Pimephales promelas Fathead minnow Pimephales notatus Bluntnose minnow Rhinichthys cataractae Longnose dace Rhinichthys atratulus Blacknose dace Semotilus atromaculalus Creek chub Couesius plumbeus Lake chub Semotilus margarita Pearl dace Catostomus catostosmus Longnose sucker 33 Status of Fish Populations and Habitat in Thunder Bay Catostomus commersoni Moxostoma anisurum Moxostoma macrolepidotum Anguilla rostrata Lota lota Eucalia inconstans Pungitius pungitius ApeItes quadracus Gasterosteus aculeatus Percopsis omiscomaycus Amblupliles rupesfrs Micropterus dolomieui Percopsis nigrornaculolus Perca flavescens Gymnocephalus cernuus Sander vitreus Etheostomaa nigrum Percina caprodes Cottus bairdi Cottus cognatus Neogobius melanostomus White sucker Silver redhorse Shorthead redhorse American eel* Burbot Brook slickleback Ninespine stickleback Fourspine stickleback* Threespine stickleback* Trout-perch Rock bass Smallmouth bass Black crappie* Yellow perch Ruffe* Walleye Johnny darter Logperch Mottled sculpin Slimy sculpin Round goby* 34